Mwesigwa, AlexTukwasibwe, StephenCummings, BryanKawalya, HakiimuKiyaga, ShahiidOkoboi, StephenCastelnuovo, BarbaraBikaitwoha, Everd ManipleKalyango, Joan N.Nsobya, Samuel L.Karamagi, CharlesByakika‑Kibwika, PaulineNankabirwa, Joaniter I.2025-04-302025-04-302025Mwesigwa, A., Tukwasibwe, S., Cummings, B., Kawalya, H., Kiyaga, S., Okoboi, S., ... & Nankabirwa, J. I. (2025). Genetic diversity and population structure of Plasmodium falciparum across areas of varied malaria transmission intensities in Uganda. Malaria Journal, 24(1), 97.https://doi.org/10.1186/s12936-025-05325-6http://hdl.handle.net/20.500.12493/2909Background: Malaria remains a significant global health threat, with sub-Saharan Africa (SSA) bearing the highest burden of the disease. Plasmodium falciparum is the predominant species in the region, leading to substantial morbidity and mortality. Despite intensified control efforts over the last two decades, P. falciparum genetic diversity and multiplicity of infections (MOI) continue to pose significant challenges to malaria elimination in the region. This study assessed P. falciparum genetic diversity and population structure in areas with low, medium, and high malaria transmission intensities in Uganda. Methods: A total of 288 P. falciparum-positive samples from children (6 months to 10 years) and adults (≥ 18 years) living in Jinja (low transmission), Kanungu (medium transmission), and Tororo (high transmission) were genotyped using seven neutral microsatellite markers. Genetic diversity was assessed based on the number of alleles (Na), allelic richness (Ar), and expected heterozygosity (He). Population structure was assessed using the fixation index, analysis of molecular variance (AMOVA), and clustering analysis. Results: High P. falciparum genetic diversity was observed across all study sites, with Kanungu exhibiting the highest mean He (0.81 ± 0.14), while Jinja and Tororo had lower mean He (0.78 ± 0.16). P. falciparum MOI varied significantly,with Tororo showing the highest mean MOI (2.5 ± 0.5) and 70% of samples exhibiting polyclonal infections, compared to Jinja’s mean MOI of 1.9 ± 0.3 and 58% polyclonal infections. Significant multilocus linkage disequilibrium (LD) was noted (p < 0.01), ranging from 0.07 in Tororo to 0.14 in Jinja. Parasite population structure showed minimal genetic differentiation (FST ranged from 0.011 to 0.021) and a low AMOVA value (0.03), indicating high gene flow. Conclusion: This study demonstrates high P. falciparum genetic diversity and MOI but low population structure, suggesting significant parasite gene flow between study sites. This highlights the need for integrated malaria control strategies across areas with varying malaria transmission intensities in Uganda.enAttribution-NonCommercial-NoDerivs 3.0 United Stateshttp://creativecommons.org/licenses/by-nc-nd/3.0/us/Plasmodium falciparumGenetic diversityMultiplicity of infectionPopulation structure and microsatellite markersArticle